View source: R/AllGenerators.R
bcbioSingleCell | R Documentation |
bcbioSingleCell
is an S4 class that extends SingleCellExperiment
, and is
designed to store a bcbio single-cell RNA-seq analysis. This class contains
read counts saved as a sparse matrix (sparseMatrix
), sample metadata, and
cell quality control metrics.
bcbioSingleCell(
uploadDir,
sampleMetadataFile = NULL,
organism = NULL,
ensemblRelease = NULL,
genomeBuild = NULL,
gffFile = NULL,
transgeneNames = NULL,
interestingGroups = "sampleName"
)
uploadDir |
|
sampleMetadataFile |
|
organism |
|
ensemblRelease |
|
genomeBuild |
|
gffFile |
|
transgeneNames |
|
interestingGroups |
|
bcbioSingleCell
.
When working in RStudio, we recommend connecting to the bcbio-nextgen run directory as a remote connection over sshfs.
Updated 2023-09-21.
Michael Steinbaugh
SingleCellExperiment::SingleCellExperiment()
.
.S4methods(class = "bcbioSingleCell")
.
uploadDir <- system.file("extdata/indrops", package = "bcbioSingleCell")
x <- bcbioSingleCell(uploadDir)
print(x)
x <- bcbioSingleCell(
uploadDir = uploadDir,
sampleMetadataFile = file.path(uploadDir, "metadata.csv")
)
print(x)
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